Nineteen RAPD primers amplified a total of 182 scorable markers in 200 samples from the four different natural populations of H.tuba, thus a total of 19 983 bands which ranged in size from 250 to 2 500 bp were generated showing homogeneous RAPD patterns, and number of scorable bands for each primer varied from 4 to 17 with an average of 5.28 bands per RAPD primer. 81.87% of the total genetic diversity was found among the four populations which contained approximately 149 polymorphic loci. 66.48%, 47.25%, 44.51%, 36.81% of the total genetic diversity were attributable to genetic differences within Beihai, Zhanjiang, Wenzhou, Lianyungang populations. Estimates of Nei’s Gene Diversity and the Shannon’s Diversity Index provided similar results of diversity, from high to low, that is, Beihai, Zhanjiang, Wenzhou, Lianyungang populations. The cluster analysis of the four populations was based on Genetic Distance, which was measured between 0.054 2-0.137 4. The results showed the populations of Beihai and Zhanjiang first assembled one branch, Wenzhou and Lianyungang then assembled another, and the two branches assembled finally.